Introduction

Quick Start

Result

  • Main Result
  • Further Analyses

    • Track Your Tasks

    1 Introduction

    GSHR is a web server provides analyses based on integrated hormone response gene sets in Arabidopsis thaliana. We developed this to facilitate cross-study and cross-platform comparisons of transcriptomic changes to hormones.

    The GSHR is user-friendly and has several features when comparing with other similar tools:

    1. The GSHR especially focuses on genes response to hormones in Arabidopsis thaliana. It supported hormone response gene sets for users to compare with their own gene lists based on Fisher's exact test.

    2. Other analysis tools are provided including cluster analysis, co-expression network, enrichment analysis of KEGG, GO and InterPro to help users unearthing the underlying biological insights of their gene lists.

    Please use the Google Chrome, Microsoft Edge or Mozilla Firefox browsers for visualization.

    2 Quick Start

    To submit the gene list, you can paste your gene list in the text area or upload a gene list file. Only one type of gene ID can be accepted (e.g. AT1G02450). If you paste your gene list, the gene list should be one ID per line. Then you can click the start analysis button to submit your task.

    3 Result

    3.1 Main Result

    3.1.1 Introduction

    The major result of GSHR is Expression Enrichment. The Expression Enrichment helps to find the most related transcriptomic studies to the input gene list. GSHR collected up- and down-regulated gene sets based on pair-wise comparisons from avaliable transcriptomic studies. If the input gene list is highly enriched in the pre-defined up- or down-regulated gene sets, the hormones and hormone-related factors potentially regulating the input gene list will be returned. The detailed descriptive and statistical information about the comparisons are also presented.

    3.1.2 Result Interpretation

    The Expression Enrichment result summary is present and you can click the link of Input Unique Gene Annotation to get all gene annotation of input gene list. Enriched studies are listed and ranked by P-value from low to high. You can click the sorting tags in front of each column to gain the sorted result you want. Selecting the checkboxs of the studies can do the further analyses of the genes enriched in the studies. The process to do further analyses presents as follows. You also can click the reset button to reselect the enriched studies.

    3.2 Further Analyses

    We provided the cluster analysis, co-expression network, KEGG, GO and InterPro enrichment for further analyses, the results were respectively showed as follows.

    3.2.1 Cluster Analysis

    3.2.2 Co-expression Network

    We constructed the co-expression network to search for the potential co-regulators of given genes. Pearson correlation coefficient was used to measure the tendency of co-expression. Notably, each pair of co-expressed genes are connected by an edge, which is highlighted in blue if they share common functions, indicating relatively strong evidence for co-regulation between the pair of genes linked.

    3.2.2.1 Arguments

    Search Depth: the maximum distance between two co-expressed genes.

    For example, given gene A in the following diagram. If search depth is 1, all genes have correlation coefficients above the cutoff with gene A are presented, such as gene B and gene C. If search depth is 2, in addition to gene B and gene C, genes co-expressed with gene B and gene C are also presented.

    Correlation Coefficient: the cutoff of co-expression, and values above this cutoff are presented in the result.

    3.2.2.2 Result Interpretation

    An interactive co-expression network will be generated by GSHR. Each pair of co-expressed genes are connected by an edge, which is highlighted in blue if they also share common functions, indicating relatively strong evidence for co-regulation between the pair of genes linked. The functions of buttons in the result page list as follows :

    Highlight Highlight the input genes in the network
    More Show more gene names
    Less Show less gene names
    Save Export the network graph in svg format
    Reset Reset the graph to the initial status
    Cofunction Highlight the co-function relationship
    Download Download the correlation coefficient table

    When you click the node in the network, it would be highlighted in the network. Meanwhile, the corresponding row in the gene table is also highlighted and vice versa. In addition, you can zoom in/out and drag the graph by your mouse.

    When you hover the pointer over one node, its neighbor nodes will be highlighted.

    3.2.3 KEGG, GO and Interpro Enrichment

    The results of KEGG, GO and Interpro enrichment are given in a similar way. Specifically, the result page of KEGG enrichment provides a link to the pathway graph where the input genes are highlighted. We only presented the KEGG enrichment result here.

    4 Track Your Tasks

    You can leave your email address, only you submit the form, a notification email will be sent to your mailbox once the task completed.

    Another method to track your job is using job id, which will be generated as the task submitted. You can enter your job id in the search box to check the status of the job. If the job is completed, the result page will show up. Currently, the job result will be kept in our server for at least two weeks.